Targeted genome editing of plants and plant cells for biomanufacturing

Abstract

Plants have provided humans with useful products since antiquity, but in the last 30 years they have also been developed as production platforms for small molecules and recombinant proteins. This initially niche area has blossomed with the growth of the global bioeconomy, and now includes chemical building blocks, polymers and renewable energy. All these applications can be described as "plant molecular farming" (PMF). Despite its potential to increase the sustainability of biologics manufacturing, PMF has yet to be embraced broadly by industry. This reflects a combination of regulatory uncertainty, limited information on process cost structures, and the absence of trained staff and suitable manufacturing capacity. However, the limited adaptation of plants and plant cells to the requirements of industry-scale manufacturing is an equally important hurdle. For example, the targeted genetic manipulation of yeast has been common practice since the 1980s, whereas reliable site-directed mutagenesis in most plants has only become available with the advent of CRISPR/Cas9 and similar genome editing technologies since around 2010. Here we summarize the applications of new genetic engineering technologies to improve plants as biomanufacturing platforms. We start by identifying current bottlenecks in manufacturing, then illustrate the progress that has already been made and discuss the potential for improvement at the molecular, cellular and organism levels. We discuss the effects of metabolic optimization, adaptation of the endomembrane system, modified glycosylation profiles, programmable growth and senescence, protease inactivation, and the expression of enzymes that promote biodegradation. We outline strategies to achieve these modifications by targeted gene modification, considering case-by-case examples of individual improvements and the combined modifications needed to generate a new general-purpose "chassis" for PMF.

Keywords: Chassis; Metabolic optimization; Modified glycosylation; Plant molecular farming; Programmable growth and senescence; Protease inactivation.

Fig. 1

Potential limitations of plant-based processes for the industry-scale manufacturing of recombinant proteins. Several features of plants that affect their use as bioreactors and reduce the efficiency of the production process could be modified by genome editing to improve product quality, overall productivity and cost-efficiency. ERAD endoplasmic reticulum-associated degradation, PTMs post-translational modifications

Fig. 2

Applications of genetic engineering and genome editing to improve plant molecular farming depending on the process stages (columns) and scales (rows). Every step during process development (columns) can benefit at the molecular, cellular and organism levels (rows). The aim of the improvements is to increase product yields, achieve authentic or compatible post-translational modifications, and integrate the use of residual biomass